Contacts of the helix formed by residues 45 - 58 (chain A) in PDB entry 2K28
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 45 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A VAL* 4.5 21.9 - - + +
9A GLU 4.7 2.4 - - - +
43A ILE* 3.6 5.1 - - - +
44A LEU* 1.3 79.1 - - - +
46A PRO* 1.4 76.7 - - - +
47A ARG* 3.2 20.0 + - - +
48A LEU* 3.2 58.9 + - + +
49A LEU* 3.9 4.4 + - - +
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Residues in contact with PRO 46 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44A LEU 3.6 6.4 - - - +
45A ASP* 1.4 92.8 - - - +
47A ARG* 1.4 80.4 + - + +
48A LEU 3.2 0.2 - - - -
49A LEU* 3.0 15.2 + - + +
50A ILE* 2.9 36.8 + - + +
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Residues in contact with ARG 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL 6.0 0.2 - - - +
9A GLU 3.8 18.4 - - - +
10A SER* 4.4 2.4 + - - -
45A ASP* 3.2 18.7 + - - +
46A PRO* 1.4 91.1 - - + +
48A LEU* 1.3 64.4 + - - +
50A ILE* 3.5 31.4 - - - +
51A ALA* 3.1 24.6 + - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.5 30.1 - - + -
10A SER* 3.6 17.0 - - - +
11A ILE* 3.4 36.7 - - + +
25A VAL* 3.9 14.1 - - + -
42A ASN 4.7 2.9 - - - +
43A ILE* 3.6 41.7 - - + -
44A LEU 4.6 0.2 - - - +
45A ASP* 3.2 39.1 + - + +
47A ARG* 1.3 76.9 - - - +
49A LEU* 1.3 57.1 + - - +
51A ALA* 3.4 3.5 + - - +
52A PHE 3.0 22.3 + - - -
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Residues in contact with LEU 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 5.0 3.6 - - + -
23A TYR* 5.6 5.4 - - + -
40A GLU* 6.1 3.1 - - + -
43A ILE* 3.6 34.5 - - + +
44A LEU 5.6 2.0 - - - +
45A ASP 4.2 8.5 - - - +
46A PRO* 3.0 14.8 + - + +
48A LEU* 1.3 76.5 - - - +
50A ILE* 1.3 60.0 + - - +
52A PHE* 3.3 21.0 - - + +
53A GLN* 3.0 41.0 + - + +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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46A PRO* 2.9 24.2 + - + +
47A ARG* 3.5 43.1 - - - +
48A LEU 3.3 0.2 - - - -
49A LEU* 1.3 71.6 - - + +
51A ALA* 1.3 66.8 + - - +
53A GLN* 3.3 19.9 + - - +
54A ASN* 3.1 40.9 + - - +
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Residues in contact with ALA 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A SER* 3.0 28.0 - - - +
11A ILE* 3.8 14.1 - - - +
47A ARG 3.1 11.2 + - - +
48A LEU 3.4 9.9 - - - +
50A ILE* 1.3 77.5 - - - +
52A PHE* 1.3 51.6 + - - +
54A ASN* 3.3 10.7 + - - +
55A ARG* 2.8 38.1 + - - +
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Residues in contact with PHE 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 3.8 17.2 - - + +
14A LYS* 3.1 31.0 - - + -
23A TYR* 3.3 36.8 - + - -
48A LEU 3.0 11.3 + - - +
49A LEU* 3.3 25.8 - - + +
51A ALA* 1.3 79.2 - - - +
53A GLN* 1.3 68.1 + - + +
55A ARG* 4.2 5.4 - - - -
56A GLU* 3.1 51.4 + - + +
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Residues in contact with GLN 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A LEU* 3.0 28.8 + - + +
50A ILE* 3.3 27.0 + - - +
52A PHE* 1.3 83.8 - - + +
54A ASN* 1.3 66.1 + - - +
56A GLU* 4.8 1.2 - - - +
57A ARG* 3.9 17.0 + - - +
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Residues in contact with ASN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.1 32.3 + - - +
51A ALA* 3.7 7.8 - - - +
53A GLN* 1.3 79.3 - - - +
55A ARG* 1.3 64.1 + - - +
57A ARG* 3.6 36.1 + - - +
58A GLN* 3.7 13.0 + - - +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ILE* 4.2 16.6 - - - +
12A GLU 2.8 26.6 + - - -
13A LYS* 3.5 28.1 - - - +
14A LYS* 3.4 18.2 + - - +
51A ALA 2.8 18.8 + - - +
52A PHE 3.3 1.5 + - - +
54A ASN* 1.3 76.3 - - - +
56A GLU* 1.3 94.8 + - - +
58A GLN* 3.1 32.0 + - - +
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A LYS* 2.9 39.3 + - - +
52A PHE* 3.1 34.6 + - + +
53A GLN 4.9 1.8 - - - +
55A ARG* 1.3 115.2 + - - +
57A ARG* 1.4 63.3 + - - +
58A GLN 3.2 8.5 + - - +
59A GLU* 4.1 7.3 + - - +
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Residues in contact with ARG 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A GLN 3.9 13.5 + - - +
54A ASN* 3.6 29.3 + - - +
55A ARG 3.3 0.2 - - - -
56A GLU* 1.4 79.0 - - - +
58A GLN* 1.4 62.0 + - - +
59A GLU* 2.9 12.1 + - - +
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Residues in contact with GLN 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A ASN 3.7 14.6 + - - +
55A ARG* 3.1 19.6 + - + +
56A GLU* 4.0 3.6 - - - +
57A ARG* 1.4 76.9 - - - +
59A GLU* 1.3 58.5 + - - +
60A GLN* 3.6 10.9 + - + +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il